You mean you have changed the namespaces by modifying the source code of the enterprise library and rebuilt it? If yes then make sure that the new assemblies are in the same location where your configuration tool is. What error are you encountering
exactly?

Did you deploy the new assemblies to the same location where the configuration tool (EntLibConfig.exe) is? Are you using as well a new build of the configuration tool or are you using the one from the installation folder integrated with
Visual Studio?

As you suggested, I found the source for configuration tool and was able to compile all the necessary app blocks and projects ( Configuration.Console, Configuration.Design and Configuration.EnvironmentalOverride )

While making the modifications, I also changed the default namespaces prefix (Microsoft.Practices.EnterpriseLibrary) to MyNamespace for all the projects/app blocks.

A few assemblies such as Microsoft.Practices.EnterpriseLibrary.Configuration.Design.HostAdapterV5, Microsoft.Practices.EnterpriseLibrary.Configuration.Design.HostAdapter, Microsoft.Practices.Unity, Microsoft.Practices.ServiceLocator ) are referenced as-is
in the resulting projects as no source is available.

When I run the resulting EntLibConfig.exe file, it opens OK but Blocks and Wizards toolbar menu items are disabled. Also, it does not load configuration files when I try to open one.

From my debugging so far, I was able to find out the issue seems to be in
EnsureCommands method of MenuCommandService
class ( Microsoft.Practices.EnterpriseLibrary.Configuration.Design.ViewModel.Services.MenuCommandService ).

The LINQ query/statement is returning an empty list while the AssemblyLocator (this.assemblyLocator.Assemblies) contained number of assemblies ( these assemblies are a mix of the newly built ones with modified namespace and some EnterpriseLibrary ones).
My assemblies are named strongly.